Sib-pair Command: list

Class	Global
Name	list | ls
Arguments	[<loc1> [[to] <locN> [$(a|q|m|h|x|A|D)[m|r]]
	where <search_string>
	where position <map_pos1> [-- | to <map_pos2>] ...

List of loci in current analysis. The "$<letter>" keyword denotes the list of of one class of locus, which can be reordered according to genetic map position (m) or in reverse (r) to the dataset ordering (mr is by reverse map order). The modifiers do not affect A and D, which are the sets of all active and all inactive loci respectively.

$a	All active binary traits
$ar	All active binary traits in reverse dataset order
$q	All active quantitative traits
$qr	All active quantitative traits in reverse dataset order
$m	All active codominant markers
$mr	All active codominant markers in reverse dataset order
$mm	All active codominant markers in map order
$mmr	All active codominant markers in reverse map order
$x	All active X-chromosomal markers
$xr	All active X-chromosomal markers in reverse dataset order
$xm	All active X-chromosomal markers in map order
$xmr	All active X-chromosomal markers in reverse map order
$h	All active haploid markers (Y or mitochondrial)
$hr	All active haploid markers in reverse dataset order
$hm	All active haploid markers in map order
$hmr	All active haploid markers in reverse map order
$A	All active loci
$D	All dropped loci

Loci can be referred to by their index in the list of loci (1..N).

Using list gives a full output with one line per locus, while ls gives an abbreviated output mimicking the results of the unix ls -F command.

The where modifier allows subsetting by an annotation matching a given search string or for a range of map positions. Map positions take the form <chr>:<coordinate> or chrXX <coordinate>. If a chromosome is not specified for a given map position, then the chromosome for the previous map position is used. A map interval may be open ended, in which case it extends to the end of the chromosome.

Example:

>> include williamsex.in

>> lis

Locus           Type Position
--------------- ---- ----------------
age              q         6
CHD              a         7
carrier          a         8
adjChol          q         9
ldl              m        10--     11

Number of marker loci=       1
Bonferroni corr. 5%  =    0.050000
Bonferroni corr. 1%  =    0.010000
Bonferroni corr. 0.1%=    0.001000

>> ls
age* CHD* carrier* adjChol* ldl
 4  active traits;  1  active markers.

>> ls $q
age* adjChol*
 2  active traits;  0  active markers.

>> ls $qr
adjChol* age*
 2  active traits;  0  active markers.

>> ls 1 2
age* CHD*
 2  active traits;  0  active markers.

>> ls carrier -- ldl
carrier* adjChol* ldl
 2  active traits;  1  active markers.

>> clear
>> include cavanaughex.in
>> lis whe pos 16:55.012
>> lis whe pos 16:54 -- 56
>> lis whe pos chr16 55.012
>> lis whe "26784604"
>> lis whe 267[789]*

[All give]

Locus        Type Position
------------ ---- ----------------
D16S3145      m         9--     10   26784604 (chr 16)

See also:

show loci	locus information
which	list positions of loci